https://github.com/reese3928/methylgsa
A Bioconductor package and shiny app for DNA methylation data length bias adjustment in gene set testing
https://github.com/reese3928/methylgsa
enrichment generalized-linear-models logistic-regression methylation ontology shiny
Last synced: 5 months ago
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A Bioconductor package and shiny app for DNA methylation data length bias adjustment in gene set testing
- Host: GitHub
- URL: https://github.com/reese3928/methylgsa
- Owner: reese3928
- Created: 2018-05-22T15:42:06.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2021-05-08T18:50:09.000Z (about 5 years ago)
- Last Synced: 2026-01-30T04:35:00.633Z (5 months ago)
- Topics: enrichment, generalized-linear-models, logistic-regression, methylation, ontology, shiny
- Language: R
- Homepage: https://bioconductor.org/packages/release/bioc/html/methylGSA.html
- Size: 7.06 MB
- Stars: 13
- Watchers: 1
- Forks: 2
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
methylGSA
===========
`methylGSA` is a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing.
The Bioconductor package can be found [here](https://bioconductor.org/packages/release/bioc/html/methylGSA.html).
The Bioconductor package vignette can be found [here](https://bioconductor.org/packages/release/bioc/vignettes/methylGSA/inst/doc/methylGSA-vignette.html).
The `methylGSA` paper can be found [here](https://doi.org/10.1093/bioinformatics/bty892).
Shiny app installation
------------
The following packages are required to be installed before launching the app.
Packages from CRAN:
```{r}
install.packages("DT")
install.packages("ggplot2")
install.packages("shinycssloaders")
```
Packages from Bioconductor:
If analyzing 450K array, `IlluminaHumanMethylation450kanno.ilmn12.hg19` needs to be installed.
```{r}
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("IlluminaHumanMethylation450kanno.ilmn12.hg19")
```
If analyzing EPIC array, `IlluminaHumanMethylationEPICanno.ilm10b4.hg19` needs to be installed.
```{r}
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("IlluminaHumanMethylationEPICanno.ilm10b4.hg19")
```
Launch the app
------------
After installation, the app can be launched with the following code:
```{r}
library(methylGSA)
methylGSA::runExample()
```
Step-by-step instructions
------------
A step-by-step instructions on the workflow of the app can be found [here](https://github.com/reese3928/methylGO-RShiny-app/raw/master/instructions.pdf).
Citation
------------
Ren, X., & Kuan, P. F. (2019). methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing. Bioinformatics, 35(11), 1958-1959.
@article{ren2019methylgsa,
title={methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing},
author={Ren, Xu and Kuan, Pei Fen},
journal={Bioinformatics},
volume={35},
number={11},
pages={1958--1959},
year={2019},
publisher={Oxford University Press}
}